Genetic variation and phylogenetic relationships of Thelymitra javanica (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia
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Abstract. Wijaya IMS, Daryono BS, Purnomo. 2020. Genetic variation and phylogenetic relationships of Thelymitra javanica Blume (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia. Biodiversitas 21: 1174-1181. Thelymitra J.R. Forst & G. Forst is a terrestrial orchid genera and mainly distributed in Australia as a center of its diversification. Moreover, Thelymitra javanica Blume is the only species of Thelymitra found in Asia, especially in Indonesia. In Australia and New Zealand, most of Thelymitra species easily found in lowland, whereas, T. javanica in Indonesia preferred to grows near the peaks of mountains around 2,000-3,000 m asl. The high altitude correlated with high light intensity and lower soil nutrients which require specific adaptation of plant to survive. The wide range of adaptation could be due to the presence of genetic variability among populations of Thelymitra. Therefore, this study was carried out to assess the genetic variability and phylogenetic relationships of T. javanica in East and Central Java. The genetic variability of Thelymitra was evaluated by molecular approaches, which is preferably utilized to determine the plant taxonomy to establish the taxonomic uncertainties. ITS-nrDNA is a popular DNA marker that widely used in phylogenetic study among various taxa. Sequences were analyses using Maximum Likelihood method with 11 in-group, 6 interspecies out-group of Thelymitra, and 2 intergeneric out-group of Thelymitrinae subtribe. The result showed that ITS-nrDNA sequences of T. javanica have no variation in nucleotide compositions and showing polytomy branch in cladogram. Thelymitra javanica also has a close relationship with Thelymitra longifolia J.R. Forst & G. Forst that are endemic to New Zealand.
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References
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White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T (eds) PCR protocols: A guide to methods and applications. Academic Press, California.
Yorifuji E, Ishikawa N, Okada H, Tsukaya H. 2015. Arundina graminifolia var. revoluta (Arethusae, Orchidaceae) has fern-type rheophyte characteristics in the leaves. J. Plant Res. 128: 239–247.
Yukawa T, Kinoshita A, Tanaka N. 2013. Molecular Identification Resolves Taxonomic Confusion in Grammatophyllum speciosum Complex (Orchidaceae). Bull. Natl. Mus. Nat. Sci., Ser. B. 39(3): 137–145.
Al-Hemaid FMA, Ali MA, Lee J, Gyulai G, Pandey AK. 2014. Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan. Bangladesh J. Plant Taxon 21(1): 33–42.
Aprilyanto V, Sembiring L. 2016. Filogenetika Molekuler: Teori dan Aplikasi. Innosain, Yogyakarta.
Arisuryanti T, Daryono BS, Handayani NSN, Aristya GR. 2017. Pelatihan Teknik Sitogenetika Genetika Molekular Bioinformatika: Analisis Sekuen DNA dan DNA Barcoding. Fakultas Biologi UGM, Yogyakarta.
Backer CA, v.d. Brink RCB. 1968. Flora of Java (spermatophytes only) vol. III. Wolters Noordhoff N.V. Groningen, Netherlands.
Backhouse GN. 2007. Are our orchids save down under? A national assessment of threatened orchids in Australia. Lankesteriana 7(1–2): 28–43.
Blume CL. 1825. Bijdragen tot de Flora van Nederlandsch Indie. Ter Lands Drukkerij, Batavia.
Brown A, Dundas P, Dixon K, Hopper S. 2008. Orchids of Western Astralia. University of Western Australia Press, Australia.
Cameron KM, Chase MW, Whitten MW, Kores PJ, Jarrell DC, Albert VA, Yukawa T, Hills HG, Goldman DH. 1999. A phylogenetic analysis of the Orchidaceae: Evidence from rbcL nucleotide sequences. American Journal of Botany 86(2): 208–224.
Chase MW, Cameron KM, Freudenstein JV, Pridgeon AM, Salazar G, Berg C, Schuiteman A. 2015. An updated classification of Orchidaceae. Botanical Journal of Linnean Society 177: 151–174.
Clements MA, Jones DL, Sharma IK, Nightingale ME, Garrat MJ, Fitzgerald KJ, Mackenzie AN, Molloy BPJ. 2002. Phylogenetic systematics of the Diuridae (Orchidaceae) based on the ITS and 5,8S coding region of nuclear ribosomal DNA. Lindleyana 13(3): 135–171.
Comber JB. 1990. Orchids of Java. Royal Botanical Garden, Kew.
Douzery EJP, Pridgeon AM, Kores P, Linder HP, Kurzweil H, Chase MW. 1999. Molecular Phylogenetics of Diseae (Orchidaceae): A Contribution from Nuclear Ribosomal ITS Sequences. American Journal of Botany 86(6): 887–899.
Dressler RL. 1993. Phylogeny and Classification of the Orchid Family. Cambridge University Press, Cambridge.
Edens-Meier R, Westhus E, Bernhardt P. 2013. Floral biology of large-flowered Thelymitra species (Orchidaceae) and their hybrids in Western Australia. Telopea Journal of Plant Sistematics 15: 165–183.
Edens-Meier R, Bernhardt P. 2014. Darwin’s Orchid: Then and Now. University of Chicago Press, Chicago.
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4): 783–791.
Hopper SD. 2009. Taxonomic turmoil down-under: Recent developments in Australian orchid systematics. Annals of Botany 104: 447–455.
Jeanes JA. 2013. An overview of Thelymitra nuda (Orchidaceae) complex in Australia including the description of six new species. Muelleria 31: 3–30.
Kalkman C. 1955. A plant-geographical analysis of the Lesser Sunda Islands. Acta Botanica Neerlandica 4(2): 200–225.
Karremans AP, Pupulin F, Gravendeel B. 2015. Specklinia dunstervillei, a new species long confused with Specklinia endotrachys (Orchidaceae: Pleurothallidinae). DOI:10.1371/journal.pone.0131971.
Keros PJ, Molvray M, Weston PH, Hopper SD, Brown AP, Cameron KM, Chase M. 2001. A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. American Journal of Botany 88(10): 1903–1914.
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111–120.
Kumar S, Stetcher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetic analysis version 7.0 for bigger data set. J. Mol. Biol. Evol. 33(7): 1870–1874.
Perkins A, Weston P. 2000. Utilization of the 18S-26S external transcribed spacer (ETS) for phylogenetic analysis of orchids. Unpublished.
Poczai P, Hyvonen J. 2010. Nuclear ribosoman spacer regions in plant phylogenetics: Problems and prospects. Mol. Biol. Rep. 37: 1897–1912.
Purnomo, Daryono BS, Shiwachi H. 2017. Phylogenetic relationship of Indonesian water yam (Dioscorea alata L.) cultivars based on DNA marker using ITS-rDNA analysis. J. Agricultural Science 9(2): 154–161.
Roberts DL, Dixon KW. 2008. Orchids. Current Biology 18(8): 325–329.
Soltis DE, Soltis PS. 1998. Choosing an approach and an appropriate gene for phylogenetics analysis. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematic in plants II: DNA sequencing. Kluwer Academic Publisher, New York.
van Steenis CGGJ. 1972. Flora of Mountain Java. LIPI, Bogor.
Weston PH, Perkins AJ, Indsto JO, Clements MA. 2014. Phylogeny of Orchidaceae Tribe Diuridae and Its Implications for the Evolution of Pollination Sistems. In: Eiden-Meier R, Bernhardt P (eds) Darwin’s Orchids: Then and Now. The University of Chicago Press, USA.
White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T (eds) PCR protocols: A guide to methods and applications. Academic Press, California.
Yorifuji E, Ishikawa N, Okada H, Tsukaya H. 2015. Arundina graminifolia var. revoluta (Arethusae, Orchidaceae) has fern-type rheophyte characteristics in the leaves. J. Plant Res. 128: 239–247.
Yukawa T, Kinoshita A, Tanaka N. 2013. Molecular Identification Resolves Taxonomic Confusion in Grammatophyllum speciosum Complex (Orchidaceae). Bull. Natl. Mus. Nat. Sci., Ser. B. 39(3): 137–145.
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